ref

strainy/gfa_operations/asm_graph_ops.py

@@ -4,15 +4,27 @@
 from strainy.clustering import build_data
 from strainy.params import *
 
+"""
+This contains functions for operation with assembly graph:
+1. add_child_edge: adds a child unitig with the same sequence as the father unitig or with the given sequence 
+(aff full path and othr clusters"
+2. add_path_links: Adds link ("full path)
+3.change_cov: recalculate coverage
+4.change_sec" recalculate sequence
+
+"""
+
+
 
 logger = logging.getLogger()
 
 
 
 def add_child_edge(edge, clN, g, cl, left, right, cons, flye_consensus, change_seq=True, insertmain=True):
     """
-    The function creates unitigs in the gfa graph
+    Adds a child unitig with the same sequence as the parental unitig or with the given sequence
     """
+    ##TODO if cons provided change_seq=True (provide seq not consensus)
     ##TODO make separare function to add gfa edge and move to gfa_ops
     consensus = flye_consensus.flye_consensus(clN, edge, cl)
     consensus_start = consensus["start"]
@@ -46,6 +58,7 @@ def add_child_edge(edge, clN, g, cl, left, right, cons, flye_consensus, change_s
 
 
 def add_path_links(graph, edge, paths,G):
+    #TODO remove G
     """
      Add gfa links between newly created unitigs forming "full path"
     """

strainy/gfa_operations/gfa_ops.py

@@ -39,7 +39,7 @@ def add_link(graph, fr, fr_or, to, to_or, w):
 
 def add_edge(graph,edge, clN, cov):
     #TODO remove edge,clN from parameters, use name instead
-    #TODO add sequ
+    #TODO add seq
     """
     Adds an empty(no sequence) segment with the specified name and coverage to the graph
     Parameters:

strainy/gfa_operations/overlap_graph_ops.py

@@ -9,6 +9,14 @@
 
 logger = logging.getLogger()
 
+"""
+This contains functions for operation with overlap graph:
+1. build_paths_graph: creates overlap graph  #TODO rename to overlap
+2. find_full_paths: finds full paths in overlap graph
+3.remove_nested(G, cons): removes nested clusters (
+4.add_path_edges : calc cluster boundaries and creates unitigs using asm.add_child_edge
+
+"""
 
 
 def build_paths_graph(cons, full_paths_roots, full_paths_leafs, cluster_distances):
@@ -22,22 +30,41 @@ def build_paths_graph(cons, full_paths_roots, full_paths_leafs, cluster_distance
         G.remove_node(0)
     except:
         pass
+    #todo move it to parental function
+    G, full_paths_roots, full_paths_leafs = \
+        remove_leaf_root_subnodes(G,full_paths_roots,full_paths_leafs)
+    G = remove_nested(G, cons)
+    G = remove_transitive(G)
+    return G
+
+
+def remove_transitive(G):
     path_remove = []
-    node_remove = []
-    for node in full_paths_leafs:
-        neighbors = list(full_paths_leafs)
+    for node in G.nodes():
+        neighbors = nx.all_neighbors(G, node)
         for neighbor in list(neighbors):
-            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff = 2):
-                if len(n_path) == 2:
-                    node_remove.append(neighbor)
+            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff = 3):
+                if len(n_path) == 3:
+                    path_remove.append(n_path)
+    for n_path in path_remove:
+        try:
+            G.remove_edge(n_path[0], n_path[1])
+        except:
+            continue
+    return G
 
-    for node in full_paths_roots:
-        neighbors = list(full_paths_roots)
+
+def remove_leaf_root_subnodes(G,full_paths_roots,full_paths_leafs):
+    node_remove = []
+    for node in full_paths_leafs+full_paths_roots:
+        if node in full_paths_leafs:
+            neighbors = list(full_paths_leafs)
+        else:
+            neighbors = list(full_paths_roots)
         for neighbor in list(neighbors):
-            for n_path in nx.algorithms.all_simple_paths(G,  neighbor,node, cutoff = 2):
+            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff = 2):
                 if len(n_path) == 2:
                     node_remove.append(neighbor)
-    G = remove_nested(G, cons)
     for node in node_remove:
         try:
             G.remove_node(node)
@@ -46,20 +73,19 @@ def build_paths_graph(cons, full_paths_roots, full_paths_leafs, cluster_distance
             full_paths_leafs.remove(node)
         except:
             continue
+    return (G,full_paths_roots,full_paths_leafs)
 
-    for node in G.nodes():
-        neighbors = nx.all_neighbors(G, node)
+
+def remove_bubbles(graph, source_nodes):
+    for node in source_nodes:
+        neighbors = list(source_nodes)
         for neighbor in list(neighbors):
-            for n_path in nx.algorithms.all_simple_paths(G, node, neighbor, cutoff = 3):
-                if len(n_path) == 3:
-                    path_remove.append(n_path)
+            for n_path in nx.algorithms.all_simple_paths(graph, node, neighbor, cutoff = 2):
+                if len(n_path) == 2:
+                    node_remove.append(neighbor)
+
+
 
-    for n_path in path_remove:
-        try:
-            G.remove_edge(n_path[0], n_path[1])
-        except:
-            continue
-    return (G)
 
 def find_full_paths(G, paths_roots, paths_leafs):
     paths = []
@@ -74,7 +100,7 @@ def find_full_paths(G, paths_roots, paths_leafs):
         for path in list(paths_nx):
             paths.append(path)
 
-    return (paths)
+    return paths
 
 
 
@@ -97,7 +123,7 @@ def remove_nested(G, cons):
                         continue
         except:
             continue
-    return (G)
+    return G
 
 def add_path_edges(edge, g, cl, ln, full_paths, G, paths_roots, paths_leafs, full_clusters, cons, flye_consensus):
     """
@@ -280,3 +306,5 @@ def paths_graph_add_vis(edge, cons, cl, full_paths_roots,
     graph_vis = gv.AGraph(graph_str)
     graph_vis.layout(prog = "dot") # TODO: this line may cause an error
     graph_vis.draw("%s/graphs/connection_graph_%s.png" % (StRainyArgs().output_intermediate, edge))
+
+